Received August 1, 2013
Modified nucleotides are universally conserved in all living kingdoms
and are present in almost all types of cellular RNAs, including tRNA,
rRNA, sn(sno)RNA, and mRNA and in recently discovered regulatory RNAs.
Altogether, over 110 chemically distinct RNA modifications have been
characterized and localized in RNA by various analytical methods.
However, this impressive list of known modified nucleotides is
certainly incomplete, mainly due to difficulties in identification and
characterization of these particular residues in low abundance cellular
RNAs. In DNA, modified residues are formed by both enzymatic reactions
(like DNA methylations, for example) and by spontaneous chemical
reactions resulting from oxidative damage. In contrast, all modified
residues characterized in cellular RNA molecules are formed by specific
action of dedicated RNA-modification enzymes, which recognize their RNA
substrate with high specificity. These RNA-modification enzymes display
a great diversity in terms of the chemical reaction and use various low
molecular weight cofactors (or co-substrates) in enzymatic catalysis.
Depending on the nature of the target base and of the co-substrate,
precise chemical mechanisms are used for appropriate activation of the
base and the co-substrate in the enzyme active site. In this review, we
give an extended summary of the enzymatic mechanisms involved in
formation of different methylated nucleotides in RNA, as well as
pseudouridine residues, which are almost universally conserved in all
living organisms. Other interesting mechanisms include thiolation of
uridine residues by ThiI and the reaction of guanine exchange catalyzed
by TGT. The latter implies the reversible cleavage of the N-glycosidic
bond in order to replace the initially encoded guanine by an
aza-guanosine base. Despite the extensive studies of RNA modification
and RNA-modification machinery during the last 20 years, our knowledge
on the exact chemical steps involved in catalysis of RNA modification
remains very limited. Recent discoveries of radical mechanisms involved
in base methylation clearly demonstrate that numerous possibilities are
used in Nature for these difficult reactions. Future studies are
certainly required for better understanding of the enzymatic mechanisms
of RNA modification, and this knowledge is crucial not only for basic
research, but also for development of new therapeutic molecules.
KEY WORDS: RNA-modification, methylation, pseudouridine,
catalytic mechanisms